---
name: "alignment-consensus"
section: "1"
platform: "linux"
package: "bali-phy"
version: "4.0-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/alignment-consensus"
---

# alignment-consensus(1)

Construct a consensus alignment to summarize an alignment sample.

## NAME

**alignment-consensus** - Construct a consensus alignment to summarize an alignment sample.

## SYNOPSIS

**alignment-consensus** alignments-file \[alignments-file ...\] \[OPTIONS\]

## DESCRIPTION

Construct a consensus alignment to summarize an alignment sample.

## ALLOWED OPTIONS:

- **-h**, **–help**

  produce help message

- **–alphabet** *arg*

  Specify the alphabet: DNA, RNA, Amino-Acids, Amino-Acids+stop, Triplets, Codons, or Codons+stop.

- **-s** *arg* (=0), **–skip** *arg* (=0)

  number of alignment samples to skip

- **-m** *arg* (=1000), **–max** *arg* (=1000)

  maximum number of alignments to analyze

- **–strict** *arg*

  ignore events below this probability

- **–cutoff** *arg*

  ignore events below this probability

- **–uncertainty** *arg*

  file-name for AU uncertainty vs level

- **–chop-to** *arg*

  keep only the first arg taxa

- **-V**, **–verbose**

  Output more log messages on stderr.

## REPORTING BUGS:

BAli-Phy online help: ⟨http://www.bali-phy.org/docs.php⟩\\c .

Please send bug reports to ⟨bali-phy-users@googlegroups.com⟩\\c .

## AUTHORS

Benjamin Redelings.